Research workbench
Crystal structure of the mouse lipin-2 M-lip domain
Analyse Crystal structure of the mouse lipin-2 M-lip domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KIQ
- Type
- protein
- Length
- 810 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidate phosphatase LPIN2
- UniProt
- Q99PI5
- Ligands
- CA
- Pockets
- 11 · best druggability 0.65
Structure
x-ray diffraction · 8 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidate phosphatase LPIN2 | protein | 80 | 48% helix, 14% strand | Q99PI5 |
| B, F | Phosphatidate phosphatase LPIN2 | protein | 82 | 50% helix, 13% strand | Q99PI5 |
| C | Phosphatidate phosphatase LPIN2 | protein | 87 | 48% helix, 15% strand | Q99PI5 |
| D, G | Phosphatidate phosphatase LPIN2 | protein | 80 | 50% helix, 14% strand | Q99PI5 |
| E | Phosphatidate phosphatase LPIN2 | protein | 83 | 47% helix, 13% strand | Q99PI5 |
| H | Phosphatidate phosphatase LPIN2 | protein | 80 | 49% helix, 14% strand | Q99PI5 |
| I | Phosphatidate phosphatase LPIN2 | protein | 80 | 48% helix, 14% strand | Q99PI5 |
| J | Phosphatidate phosphatase LPIN2 | protein | 76 | 50% helix, 16% strand | Q99PI5 |
Ligands and binding sites
- CA · Calcium ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.65 | 0.80 | 42 | empty |
| 2 | 182 | 0.65 | 0.85 | 29 | empty |
| 3 | 473 | 0.63 | 0.76 | 56 | empty |
| 4 | 144 | 0.60 | 0.84 | 23 | empty |
| 5 | 119 | 0.60 | 0.85 | 25 | empty |
Interfaces
17 interfaces between chains.
- C–D · 1363 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 1354 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 1344 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1334 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 720 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q99PI5
- Elsewhere: RCSB PDB 7KIQ · PDBe 7KIQ · UniProt Q99PI5
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